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Related Concept Videos

Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Related Experiment Video

Updated: May 30, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

A coarse-grained force field for Protein-RNA docking.

Piotr Setny1, Martin Zacharias

  • 1Physics Department T38, Technical University Munich, James-Franck-Strasse 1, 85748 Garching, Germany. piotr.setny@tum.de

Nucleic Acids Research
|August 18, 2011
PubMed
Summary

This study introduces a new computational method for predicting the structure of protein-RNA complexes. The coarse-grained force field enables fast and efficient protein-RNA docking without prior geometric knowledge.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: May 30, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology
  • Molecular Biophysics

Background:

  • Functional non-coding RNA (ncRNA) molecules are crucial in biological processes.
  • ncRNAs interact with proteins to form ribonucleoprotein complexes.
  • Understanding these complex structures is vital but challenging due to experimental data limitations.

Purpose of the Study:

  • To present a novel coarse-grained force field for protein-RNA docking.
  • To enable accurate prediction of complex structures using computational methods.
  • To facilitate the integration of fragmented or multi-resolution experimental data.

Main Methods:

  • Implementation of a coarse-grained force field within the ATTRACT program.
  • Utilizing energy minimization for rotational and translational degrees of freedom.
  • Incorporating structural flexibility for enhanced accuracy.
  • Performing systematic docking searches without prior geometric assumptions.

Main Results:

  • The developed coarse-grained force field allows for fast and efficient protein-RNA docking.
  • The method enables systematic structure prediction of ribonucleoprotein complexes.
  • It effectively integrates and refines limited or multi-resolution experimental data.

Conclusions:

  • The new computational approach significantly advances the prediction of protein-RNA complex structures.
  • This method provides a powerful tool for structural biologists and computational chemists.
  • It overcomes limitations of experimental data and enhances our understanding of ncRNA function.